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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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mzR Resource Report Resource Website |
mzR (RRID:SCR_002856) | software resource | Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. | standalone software, mac os x, unix/linux, windows, r, data import, infrastructure, mass spectrometry, metabolomics, proteomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02654 | SCR_002856 | mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files | 2026-02-14 02:00:33 | 0 | ||||||||
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BiGGR Resource Report Resource Website |
BiGGR (RRID:SCR_002854) | software resource | Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs. | standalone software, mac os x, unix/linux, windows, r, metabolomics, network, visualization, metabolic reconstruction, model |
uses: BiGG Database is listed by: OMICtools has parent organization: Bioconductor |
PMID:25806817 | Free, Freely available, Available for download | OMICS_02655 | SCR_002854 | BiGGR - Constraint based modeling in R using metabolic reconstruction databases | 2026-02-14 02:00:33 | 0 | |||||||
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PAPi Resource Report Resource Website 50+ mentions |
PAPi (RRID:SCR_002857) | software resource | An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:20929912 | Free, Freely available, Available for download | OMICS_02653 | SCR_002857 | PAPi - Predict metabolic pathway activity based on metabolomics data, Pathway Activity Profiling | 2026-02-14 02:00:20 | 53 | |||||||
|
National Academies Press Resource Report Resource Website 10+ mentions |
National Academies Press (RRID:SCR_002844) | institution | The National Academies Press (NAP) was created by the National Academies to publish the reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council, all operating under a charter granted by the Congress of the United States. The NAP publishes more than 200 books a year on a wide range of topics in science, engineering, and health, capturing the most authoritative views on important issues in science and health policy. The institutions represented by the NAP are unique in that they attract the nation's leading experts in every field to serve on their award-winning panels and committees. This is the right place for definitive information on everything from space science to animal nutrition. Many books can be read on-line for free. NAP also offers many titles in electronic Adobe PDF format. Hundreds of these books can be downloaded for free by the chapter or the entire book, while others are available for purchase. Sponsors: This resource is supported by The National Academies. | engineering, academy, animal, medicine, national, nutrition, research, science | Free, Freely available | ISNI: 0000 0004 0466 615X, Wikidata: Q6970107, grid.431670.7, nif-0000-25219 | https://ror.org/02a6ztn45 | SCR_002844 | NAP | 2026-02-14 02:00:27 | 40 | ||||||||
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University of Coimbra; Coimbra; Portugal Resource Report Resource Website |
University of Coimbra; Coimbra; Portugal (RRID:SCR_002842) | UC | university | Public university in Coimbra, Portugal that offers degree programs in a variety of fields including law, medicine, science and technology, pharmaceuticals, and sports sciences. | public university, portugal, degree program |
is parent organization of: EPILAB is parent organization of: University of Coimbra ViralVector Core Facility is parent organization of: University of Coimbra Department of Chemistry NMR Core facility |
Free | nlx_155543, ISNI:0000 0000 9511 4342, Wikidata:Q368643, Crossref funder ID:501100007474, grid.8051.c | https://ror.org/04z8k9a98 | SCR_002842 | University of Coimbra, Universidade de Coimbra | 2026-02-14 02:00:33 | 0 | ||||||
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General Clinical Research Centers Program Resource Report Resource Website 10+ mentions |
General Clinical Research Centers Program (RRID:SCR_002847) | GCRC | funding resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities. | clinical research program, career development |
has parent organization: National Center for Research Resources has parent organization: National Institutes of Health |
NCRR | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25308 | SCR_002847 | General Clinical Research Centers, General Clinical Research Centers (GCRC) | 2026-02-14 02:00:20 | 35 | ||||||
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OBD-PKB Interface Resource Report Resource Website 1+ mentions |
OBD-PKB Interface (RRID:SCR_002882) | data or information resource, ontology, controlled vocabulary | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF project. | data, disease, neurodegenerative, software | has parent organization: University of California at Berkeley; Berkeley; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25570 | SCR_002882 | OBD-PKB Interface | 2026-02-14 02:00:34 | 1 | ||||||||
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CVXOPT - Python Software for Convex Optimization Resource Report Resource Website 1+ mentions |
CVXOPT - Python Software for Convex Optimization (RRID:SCR_002918) | CVXOPT | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. | convex optimization, python | has parent organization: University of California at Los Angeles; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30018 | SCR_002918 | CVXOPT - Python Software for Convex Optimization | 2026-02-14 02:00:20 | 2 | |||||||
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Brazilian Ministry of Science Technology and Innovation Resource Report Resource Website 1+ mentions |
Brazilian Ministry of Science Technology and Innovation (RRID:SCR_002876) | MCTI, MCT | government granting agency | is parent organization of: National Laboratory for Scientific Computing; Rio de Janeiro; Brazil | SCR_002876 | Tecnologia e Inovação, Ministry of Science Technology and Innovation (Brazil), Ministério da Ciência, Ministério da Ciência e Tecnologia - Brazil, Ministry of Science and Technology (Brazil) | 2026-02-14 02:00:34 | 7 | |||||||||||
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British Heart Foundation Resource Report Resource Website 100+ mentions |
British Heart Foundation (RRID:SCR_002905) | BHF | institution | British charity and fundraiser for cardiovascular research. | cardiovascular research, coronary heart disease, fundraising | Crossref funder ID: 501100000274, ISNI: 0000 0001 0540 7035, nlx_82345, grid.452924.c, Wikidata: Q4970039 | https://ror.org/02wdwnk04 | SCR_002905 | 2026-02-14 02:00:35 | 130 | |||||||||
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University of Cologne; Cologne; Germany Resource Report Resource Website 1+ mentions |
University of Cologne; Cologne; Germany (RRID:SCR_002903) | UoC | university | Public university in Germany that offers degrees in law, management and business, the arts and humanities, and human sciences. | public university, germany, degree program |
is parent organization of: TargetCaller is parent organization of: CGARS is parent organization of: ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins is parent organization of: Dictyostelium discoideum genome database is parent organization of: Gentle is parent organization of: Dictyostelium discoideum genome database is parent organization of: University of Cologne Center for Genomics (CCG) Core Facility |
grid.6190.e, ISNI:0000 0000 8580 3777, Wikidata:Q54096, nlx_14953 | https://ror.org/00rcxh774 | http://www.portal.uni-koeln.de/uoc_home.html?&L=1 | SCR_002903 | University of Cologne, Universitat zu Koln | 2026-02-14 02:00:20 | 2 | ||||||
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CNVassoc Resource Report Resource Website 1+ mentions |
CNVassoc (RRID:SCR_002901) | software resource | Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21609482 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02609 | SCR_002901 | CNVassoc: Association analysis of CNV data | 2026-02-14 02:00:27 | 1 | |||||||
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University of Colorado Boulder; Colorado; USA Resource Report Resource Website 1+ mentions |
University of Colorado Boulder; Colorado; USA (RRID:SCR_003114) | university | Public university that offers degrees in the sciences, humanities, and social sciences. | university, research university, public university, colorado, degree |
is related to: Beta Cell Biology Consortium is related to: ELOKA has parent organization: University of Colorado; Colorado; USA is parent organization of: University of Colorado at Boulder Labs and Facilities is parent organization of: Community Surface Dynamics Modeling System is parent organization of: National Snow and Ice Data Center is parent organization of: IMOD is parent organization of: University of Colorado at Boulder, Department of Neuroscience is parent organization of: NeuraLinksPlus is parent organization of: Emergent is parent organization of: Standalone hamming is parent organization of: CU Boulder Electron Microprobe Laboratory is parent organization of: CU Boulder Institute for Behavioral Genetics is parent organization of: SeqTrace is parent organization of: QIIME is parent organization of: Colorado University at Boulder Shared Instrumentation in Nanofabrication and Characterization Core Facility is parent organization of: Colorado University at Boulder JILA Keck Lab and Fabrication Core Facility is parent organization of: Colorado University at Boulder Biochemistry Shared Instruments Pool Core Facility is parent organization of: Colorado University at Boulder Center for Infrastructure, Energy, and Space Testing Core Facility is parent organization of: Colorado University at Boulder Light Microscopy Core Facility is parent organization of: Colorado University at Boulder EM Services Core Facility is parent organization of: Colorado University at Boulder Green Labs Core Facility is parent organization of: Colorado University at Boulder Central Analytical Mass Spectrometry Core Facility is parent organization of: Colorado University at Boulder Intermountain Neuroimaging Consortium Core Facility is parent organization of: Colorado University at Boulder Green Labs Core Facility is parent organization of: Colorado University at Boulder BioChemistry Krios Electron Microscopy Core Facility is parent organization of: University of Colorado Boulder Chemical and Bio. Engineering instrument and electronics Core Facility is parent organization of: University of Colorado Boulder High Performance Computing PetaLibrary Core Facility is parent organization of: University of Colorado Boulder Earth Systems Stable Isotope Lab Core Facility is parent organization of: University of Colorado Boulder Organic Geochemistry Laboratory Core Facility is parent organization of: University of Colorado Boulder BioCore Core Facility is parent organization of: University of Colorado Boulder CU Thermochronology Research and Instrumentation Lab Core Facility is parent organization of: Colorado University at Boulder Soft Materials Research Center X-Ray Diffraction Facility Core Facility is parent organization of: University of Colorado Boulder Raman Microspectroscopy Lab Core Facility is parent organization of: Colorado University at Boulder Facility for Electron Microscopy of Materials Core Facility is parent organization of: Colorado University at Boulder Materials Instrumentation and Multimodal Imaging Core Facility is parent organization of: Colorado University at Boulder BioFrontiers Next-Gen Sequencing Facility Core Facility is parent organization of: Colorado University at Boulder Flow Cytometry Shared Core Facility is parent organization of: Colorado University at Boulder Macromolecular X-ray Crystallography Core Facility is parent organization of: University of Colorado Anschutz Medical Campus ImmunoMicro Flow Cytometry Core Facility is parent organization of: Colorado University at Boulder High Throughput Screening Core Facility is parent organization of: University of Colorado Boulder Polymeric and Optical Materials Characterization Shared Core Facility is parent organization of: SHARCQ is parent organization of: University of Colorado Boulder Geomicrobiology Lab Core Facility is parent organization of: University of Colorado Boulder Intermountain Neuroimaging Consortium Core Facility |
Free, Freely available | nlx_10266 | https://ror.org/02ttsq026 | SCR_003114 | CU Boulder, UC Boulder, University of Colorado Boulder, CU-Boulder | 2026-02-14 02:00:22 | 3 | |||||||
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SURPI Resource Report Resource Website 10+ mentions |
SURPI (RRID:SCR_003071) | SURPI | software resource | Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples. | pipeline, cloud based pipeline, pathogen identification |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
PMID:24899342 | OMICS_04623 | https://github.com/chiulab/surpi | SCR_003071 | Sequence-based Ultra-Rapid Pathogen Identification | 2026-02-14 02:00:38 | 13 | ||||||
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FAS-DPD Resource Report Resource Website |
FAS-DPD (RRID:SCR_003068) | FAS-DPD | software resource | Software program to design degenerate primers for PCR. | command-line, java, primer, pcr, degenerate primer |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533783 | Free, Available for download, Freely available | OMICS_02340 | SCR_003068 | family-specific degenerate primer design | 2026-02-14 02:00:38 | 0 | ||||||
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pFind Resource Report Resource Website 100+ mentions |
pFind (RRID:SCR_003011) | software resource | A search engine system for automated peptide and protein identification from tandem mass spectra. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
PMID:17702057 | OMICS_02467 | SCR_003011 | 2026-02-14 02:00:21 | 118 | |||||||||
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BioCaster Ontology Resource Report Resource Website |
BioCaster Ontology (RRID:SCR_003122) | BCO | data or information resource, ontology, controlled vocabulary | A multilingual application ontology aimed at the early detection of public health events in the media. It aims to describe the terms and relations necessary to detect and risk assess public health events in the grey literature at an early stage; and bridge the gap between the (multilingual) grey literature and existing standards in biomedicine. The BCO focuses on the usage of terms and relations within informal unstructured reports which are often made at a pre-diagnostic stage of a disease outbreak by non-medically trained reporters. This is done to provide monitoring and early warning about public health hazards from online media reports. | public health, text-mining, infectious disease, owl, skos, database |
has parent organization: Google Code has parent organization: BioCaster |
Infectious disease | Free, Available for download, Freely available | nlx_156797 | http://born.nii.ac.jp/_dev/static/ontology | SCR_003122 | biocaster-ontology | 2026-02-14 02:00:40 | 0 | |||||
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Genetic Analysis Package Resource Report Resource Website 1+ mentions |
Genetic Analysis Package (RRID:SCR_003006) | software resource | GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. | genetic, analysis, package, data, population, family, calculation, family, disease, aggregation, kinship, environmental, covariate, haplotype, marker | nif-0000-30271 | SCR_003006 | GAP | 2026-02-14 02:00:28 | 1 | ||||||||||
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tweeDEseq Resource Report Resource Website 1+ mentions |
tweeDEseq (RRID:SCR_003038) | software resource | Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. | standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23965047 | Free, Available for download, Freely available | OMICS_02406, biotools:tweedeseq | https://bio.tools/tweedeseq | SCR_003038 | tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions | 2026-02-14 02:00:29 | 4 | ||||||
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JAX Neuroscience Mutagenesis Facility Protocols Resource Report Resource Website |
JAX Neuroscience Mutagenesis Facility Protocols (RRID:SCR_003021) | NMF Protocols | data or information resource, experimental protocol, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information | mutant mouse strain, genetically-modified mouse, motor system function, impairment of function, eye disease, eye disorder, ophthalmological disorder, ophthalmic disorder, ocular disease, disease of eye, epilepsy, epileptic seizure, seizure disorder, gustatory system function, taste system function, bioinformatics, acoustic startle response, auditory brainstem response, creatine kinase, development, eye, vision, gait, gustation, observation, seizure, mutagenesis, n-ethyl-n-nitrosourea, es cell mutagenesis, ems, genetics, phenotyping | has parent organization: JAX Neuroscience Mutagenesis Facility | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00527 | SCR_003021 | JAX Protocols, Protocols of the NMF, Protocols of the Neuroscience Mutagenesis Facility, JAX NMF Protocols | 2026-02-14 02:00:28 | 0 |
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